Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-27 12:03 -0400 (Wed, 27 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4612 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 797/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemma.R 3.5.4 (landing page) Ogan Mancarci
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the gemma.R package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemma.R.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: gemma.R |
Version: 3.5.4 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R |
StartedAt: 2025-08-26 17:24:14 -0400 (Tue, 26 Aug 2025) |
EndedAt: 2025-08-26 17:26:51 -0400 (Tue, 26 Aug 2025) |
EllapsedTime: 157.2 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R ### ############################################################################## ############################################################################## * checking for file ‘gemma.R/DESCRIPTION’ ... OK * preparing ‘gemma.R’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘gemma.R.Rmd’ using rmarkdown Quitting from gemma.R.Rmd:325-328 [unnamed-chunk-15] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `.body()`: ! https://gemma.msl.ubc.ca/rest/v2/resultSets/550248 500: Internal server error. --- Backtrace: ▆ 1. └─gemma.R::get_differential_expression_values("GSE46416") 2. └─base::lapply(...) 3. └─gemma.R (local) FUN(X[[i]], ...) 4. └─gemma.R:::.getResultSets(x, memoised = memoised) 5. └─gemma.R:::mem.getResultSets(...) 6. ├─gemma.R (local) mem_call(...) 7. │ ├─base::withVisible(eval(mc, parent.frame())) 8. │ └─base::eval(mc, parent.frame()) 9. │ └─base::eval(mc, parent.frame()) 10. └─gemma.R (local) `<fn>`(...) 11. └─gemma.R:::.body(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'gemma.R.Rmd' failed with diagnostics: https://gemma.msl.ubc.ca/rest/v2/resultSets/550248 500: Internal server error. --- failed re-building ‘gemma.R.Rmd’ --- re-building ‘metadata.Rmd’ using rmarkdown Quitting from metadata.Rmd:131-142 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `sum()`: ! invalid 'type' (list) of argument --- Backtrace: ▆ 1. └─... %>% sum ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'metadata.Rmd' failed with diagnostics: invalid 'type' (list) of argument --- failed re-building ‘metadata.Rmd’ --- re-building ‘metanalysis.Rmd’ using rmarkdown Quitting from metanalysis.Rmd:225-238 [unnamed-chunk-13] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `.body()`: ! https://gemma.msl.ubc.ca/rest/v2/resultSets/515364 500: Internal server error. --- Backtrace: ▆ 1. ├─parkin_contrasts$result.ID %>% ... 2. ├─BiocGenerics::lapply(...) 3. └─base::lapply(...) 4. └─FUN(X[[i]], ...) 5. └─gemma.R::get_differential_expression_values(resultSets = x) 6. └─base::lapply(...) 7. └─gemma.R (local) FUN(X[[i]], ...) 8. └─gemma.R:::.getResultSets(x, memoised = memoised) 9. └─gemma.R:::mem.getResultSets(...) 10. ├─gemma.R (local) mem_call(...) 11. │ ├─base::withVisible(eval(mc, parent.frame())) 12. │ └─base::eval(mc, parent.frame()) 13. │ └─base::eval(mc, parent.frame()) 14. └─gemma.R (local) `<fn>`(...) 15. └─gemma.R:::.body(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'metanalysis.Rmd' failed with diagnostics: https://gemma.msl.ubc.ca/rest/v2/resultSets/515364 500: Internal server error. --- failed re-building ‘metanalysis.Rmd’ SUMMARY: processing the following files failed: ‘gemma.R.Rmd’ ‘metadata.Rmd’ ‘metanalysis.Rmd’ Error: Vignette re-building failed. Execution halted